Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g00890.N4
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6095
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Found at i:38 original size:16 final size:16
Alignment explanation
Indices: 17--169 Score: 93
Period size: 16 Copynumber: 9.7 Consensus size: 16
7 CAAATTTCAA
17 AACTTACATAATACAT
1 AACTTACATAATACAT
**
33 AACTTACATAATTTA-
1 AACTTACATAATACAT
** *
48 AAGAT-CA-AATTTCAT
1 AACTTACATAA-TACAT
*
63 AACTTAGATAATACAT
1 AACTTACATAATACAT
* **
79 AACTTATATAATTTA-
1 AACTTACATAATACAT
** *
94 AAGAT-CA-AATTTCAT
1 AACTTACATAA-TACAT
109 AACTTACATAATTTACAT
1 AACTTACATAA--TACAT
*
127 AACTTACATAATAAAT
1 AACTTACATAATACAT
*
143 ATCTTACATAATACAT
1 AACTTACATAATACAT
*
159 GACTTACATAA
1 AACTTACATAA
170 CTTTATTATA
Statistics
Matches: 104, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
13 4 0.04
14 9 0.09
15 12 0.12
16 59 0.57
17 4 0.04
18 16 0.15
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:42 original size:9 final size:9
Alignment explanation
Indices: 17--172 Score: 76
Period size: 9 Copynumber: 17.6 Consensus size: 9
7 CAAATTTCAA
17 AACTTACAT
1 AACTTACAT
26 AA--TACAT
1 AACTTACAT
33 AACTTACAT
1 AACTTACAT
* *
42 AATTTAAAGAT
1 AACTT--ACAT
* *
53 CAAATTTCAT
1 -AACTTACAT
*
63 AACTTAGAT
1 AACTTACAT
72 AA--TACAT
1 AACTTACAT
*
79 AACTTATAT
1 AACTTACAT
* *
88 AATTTAAAGAT
1 AACTT--ACAT
* *
99 CAAATTTCAT
1 -AACTTACAT
109 AACTTACAT
1 AACTTACAT
*
118 AATTTACAT
1 AACTTACAT
127 AACTTACAT
1 AACTTACAT
*
136 AA--TAAAT
1 AACTTACAT
*
143 ATCTTACAT
1 AACTTACAT
152 AA--TACAT
1 AACTTACAT
*
159 GACTTACAT
1 AACTTACAT
168 AACTT
1 AACTT
173 TATTATACTT
Statistics
Matches: 108, Mismatches: 25, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
7 24 0.22
9 66 0.61
10 4 0.04
11 6 0.06
12 8 0.07
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.36
Consensus pattern (9 bp):
AACTTACAT
Found at i:68 original size:46 final size:46
Alignment explanation
Indices: 1--138 Score: 231
Period size: 46 Copynumber: 3.0 Consensus size: 46
*
1 AAAGATCAAATTTCAAAACTTACATAATACATAACTTACATAATTT
1 AAAGATCAAATTTCATAACTTACATAATACATAACTTACATAATTT
* *
47 AAAGATCAAATTTCATAACTTAGATAATACATAACTTATATAATTT
1 AAAGATCAAATTTCATAACTTACATAATACATAACTTACATAATTT
93 AAAGATCAAATTTCATAACTTACATAATTTACATAACTTACATAAT
1 AAAGATCAAATTTCATAACTTACATAA--TACATAACTTACATAAT
139 AAATATCTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
46 69 0.81
48 16 0.19
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (46 bp):
AAAGATCAAATTTCATAACTTACATAATACATAACTTACATAATTT
Found at i:4228 original size:32 final size:31
Alignment explanation
Indices: 4192--4259 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
4182 GAATGAATGT
* *
4192 TTTTGGCTGTATTTTTATGCTAAATTTGTTGA
1 TTTTGGCTGCA-TTTCATGCTAAATTTGTTGA
* *
4224 TTTTGGTTGCATTTCATGCTATATTTGTTGA
1 TTTTGGCTGCATTTCATGCTAAATTTGTTGA
4255 TTTTG
1 TTTTG
4260 ATTGGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.16, C:0.07, G:0.19, T:0.57
Consensus pattern (31 bp):
TTTTGGCTGCATTTCATGCTAAATTTGTTGA
Found at i:4244 original size:31 final size:31
Alignment explanation
Indices: 4208--4273 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
4198 CTGTATTTTT
* *
4208 ATGCTAAATTTGTTGATTTTGGTTGCATTTC
1 ATGCTAAATTTGTTGATTTTGATTGCATTTA
* *
4239 ATGCTATATTTGTTGATTTTGATTGGATTTA
1 ATGCTAAATTTGTTGATTTTGATTGCATTTA
4270 ATGC
1 ATGC
4274 AAGAAGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.21, C:0.08, G:0.20, T:0.52
Consensus pattern (31 bp):
ATGCTAAATTTGTTGATTTTGATTGCATTTA
Done.